runGO: Run gene set enrichement on Gene Ontology categories

In sansomlab/gsfisher: Geneset Fisher

Run gene set enrichement on Gene Ontology categories

Description

A wrapper function to run Fisher's test for enrichement on Gene Ontology (GO) categories. Depends on the bioconductor org.xx.eg.db and GO.db packages.

Usage

runGO(
  foreground_ids,
  background_ids,
  gene_id_type = c("entrez", "ensembl"),
  species = c("hs", "mm"),
  ...
)

Arguments

foreground_ids	A list of ENTREZ ids of interest (e.g. significantly differentially expressed genes).
background_ids	A list of background ENTREZ ids. against which enrichment will be tested (i.e., the gene universe). (see fetchAnnotation).
gene_id_type	Either "entrez" (default") or "ensembl".
species	Species identifier (only "hs" or "mm" are supported).

Author(s)

Steve Sansom

See Also

runFisherTests.

Examples

# TODO
## Not run: 
# TODO

## End(Not run)

sansomlab/gsfisher documentation built on July 7, 2022, 4:21 a.m.